LS Package

LS Package

Lions SAXS package contains all the necessary for SAXS treatment and SAXS modelization

LSneutron Module

pySAXS.LS.LSneutron.PeneDepth(S, N, lamda, rho)[source]
pySAXS.LS.LSneutron.ScaLengthDensity(S, N, rho)[source]

return the electron density and the scattering length density

pySAXS.LS.LSneutron.getMolMass(S, N)[source]

This function returns the molar mass a chemical formula in the form ‘C 6 H 6 O 2 N 1’

pySAXS.LS.LSneutron.getTotalScaLen(S, N)[source]
pySAXS.LS.LSneutron.getTotalXS(S, N, lamda)[source]

LSsca Module

pySAXS python routines for small angle xray scattering. This is the core of pySAXS containing usefull function for SAXS data treatment, tested and optimized amplitude and form factor

pySAXS.LS.LSsca.Cubedre(a, L)[source]

return the 3D coordinates of the 6 submits of a cube

pySAXS.LS.LSsca.Dalpha(par)[source]

This function returns a modified lognormal distribution for the array r with an averaga size rm and a standard deviation sigma

pySAXS.LS.LSsca.Decaedre(a, b)[source]

returne the 3D cartesian coordinates of the seven sumits of decahedra

pySAXS.LS.LSsca.Dexpon(par)[source]

This function returns a modified lognormal distribution for the array r with an averaga size rm and a standard deviation sigma

pySAXS.LS.LSsca.Dgauss(par)[source]

This function returns a gaussian distribution for the array r with an averaga size rm and a standard deviation sigma.

pySAXS.LS.LSsca.Dlognormal(par)[source]

This function returns a modified lognormal distribution for the array r with an averaga size rm and a standard deviation sigma

pySAXS.LS.LSsca.Doublet_Multiplet(a)[source]
pySAXS.LS.LSsca.Dshultz(r, rav, z)[source]

This function returns a shultz distribution for the array r with rav, z as parameter

pySAXS.LS.LSsca.F1(q, R)[source]

This function returns a scattering amplitude of a sphere of radius R for q

pySAXS.LS.LSsca.F2(q, R1, R2)[source]

This function returns a scattering amplitude of an empty shell of internal radius R2 and external radius R2 for q

pySAXS.LS.LSsca.F3(q, R, rho)[source]

This function returns the scattering amplitude of spherically symetric shells of internal radius Ri and scattering length density rhoi for q

pySAXS.LS.LSsca.F3elli(q, R, e, rho)[source]
pySAXS.LS.LSsca.FaceTri(R)[source]

return the 5 faces of the triedre

pySAXS.LS.LSsca.FacesDeca(R)[source]

return the faces of the decaedra R

pySAXS.LS.LSsca.FacesHexa(R)[source]

return the faces of the hexaedre_cyl R, fonctionne pour le deforme egalement

pySAXS.LS.LSsca.FacesHexa_creux_def(R, Rin)[source]

return the faces of the hexaedre_cyl R

pySAXS.LS.LSsca.FacesTetraedre(R)[source]

returns the faces of the tetraedre

pySAXS.LS.LSsca.Facescube(R)[source]

return the 6 faces of the Cubedre

pySAXS.LS.LSsca.Faceshexaedre(R)[source]

returns the 6 faces of the hexaedre

pySAXS.LS.LSsca.Facesoctaedre(R)[source]

returns the faces of the octaedre

pySAXS.LS.LSsca.Guinier(q, I0, Rg)[source]

Guinier function

pySAXS.LS.LSsca.Hexaedre(a)[source]

returns the 3D coordinates of the 8 summits of an hexaedre side length a

pySAXS.LS.LSsca.Hexaedre_cyl(a, L)[source]

return the 3D coordinates of the 12 submits of an hexaedre_cyl

pySAXS.LS.LSsca.Hexaedre_def(a, b, L)[source]

return the 3D coordinates of the 12 submits of an hexaedre_cyl deforme (a,b) au lieu de (a,a)

pySAXS.LS.LSsca.Idqc(q, rho1, rho2, rho3, al1, al2, al3, Phi1, Phi2, RG0, RGsig, R1, sigR1, R3, sigR3, taoL, taoS, scale, reduc)[source]
pySAXS.LS.LSsca.Multiplet(q, L, rho, R)[source]
pySAXS.LS.LSsca.Normale(Face)[source]

returns the oriented and normalized normal to the face

pySAXS.LS.LSsca.Octaedre(a)[source]

returns the 3D coordinates of the 6 summits of a octaaedre of side length a

pySAXS.LS.LSsca.P1(q, R)[source]

This function returns the form factor of a sphere of radius R for q

pySAXS.LS.LSsca.P11(q, R, L)[source]
pySAXS.LS.LSsca.P11_int(q, R, L)[source]
pySAXS.LS.LSsca.P1Sqdist(q, type, rm, sigma, eta, tao)[source]

This function returns the form factor of a dsitribution of spheres of radius R for q

pySAXS.LS.LSsca.P1dist(q, Dfunc, par)[source]

This function returns the form factor of a dsitribution of spheres of radius R for q

pySAXS.LS.LSsca.P2(q, R1, R2)[source]

This function returns the form factor of an empty shell of internal radius R2 and external radius R2 for q

pySAXS.LS.LSsca.P3(q, R, rho)[source]

This function returns the form factor of spherically symetric shells of internal radius Ri and scattering length density rhoi for q

pySAXS.LS.LSsca.P3elli(q, R, e, rho)[source]

This function returns the form factor of spherically symetric shells of internal radius Ri and scattering length density rhoi for q

pySAXS.LS.LSsca.P5(q, R, e)[source]

This function returns the form factor of an ellipsoid of revolution with semi-axes R, R and e*R for q

pySAXS.LS.LSsca.P5_conc_int(q, R, e, rho)[source]
pySAXS.LS.LSsca.P5_int(q, R, e)[source]
pySAXS.LS.LSsca.P5conc(q, R, e, rho)[source]

This function returns the form factor of an concentric ellipsoid of revolutions with semi-axes R, R and e*R for q

pySAXS.LS.LSsca.P5dist(q, type, rm, sigma, e)[source]

This function returns the form factor of a dsitribution of ellipses with semi-axes R, R and e*R for q

pySAXS.LS.LSsca.PS(a, b)[source]

return the scalar product of two vetors

pySAXS.LS.LSsca.PV(u, v)[source]

return the vector orthogonal to u and v

pySAXS.LS.LSsca.Pcyl(q, R, L)[source]

Optimized version of P11 OS This function calculates the P(q) of a cylinder of length L and radius R

pySAXS.LS.LSsca.Pcylcos(q, R, L)[source]

Optimized version of P11 OS This function calculates the P(q) of a cylinder of length L and radius R

pySAXS.LS.LSsca.Pcylcouche(q, rho, R, L)[source]

This function calculates the scaled by volume square and scattering length density P(q) of a cylinder of inner length L1 and radius R1 and outer length L2 and radius R2. It is thus more versatile than Pcylcreux

pySAXS.LS.LSsca.Pcylcreux(q, Ri, Ro, L)[source]

This function calculates the P(q) normalized to one at q=0 of an hollow cylinder of length L inner radius Ri and outer radius Ro

pySAXS.LS.LSsca.Pcylcreuxcan(q, a, Ri, Ro, L)[source]
pySAXS.LS.LSsca.Pcylcreuxqcq(q, Ri, L, alp, b, x0, delt)[source]

contient une erreur en date du 30 avril 2009 connue mais a corriger This function calculates the P(q) normalized to one at q=0 of an hollow cylinder of length L inner radius Ri and outer radius Ro

pySAXS.LS.LSsca.Pcylh(q, R, L)[source]

Optimized version of P11 OS This function calculates the P(q) of a cylinder of length L and radius R with two hemispheres of redaisu R as cap ends is associated with dPcylh

pySAXS.LS.LSsca.Pcylmulti(q, R, rho, L, rhos)[source]

This function calculates at the absolute scale the P(q) of a cylinder of length L and and multilayers R of density Rho the last one being solvent

pySAXS.LS.LSsca.Pcylvb(q, R, L)[source]

This function calculates the P(q) normalized to one at q=0 of a cylinder of length L and radius R

pySAXS.LS.LSsca.PdqHexa3(q, R, L, N)[source]
pySAXS.LS.LSsca.PdqHexacoq(q, Ri, Ro, L, N)[source]
pySAXS.LS.LSsca.Pdqhexa(q, a, N)[source]
pySAXS.LS.LSsca.Pdqocta(q, a, N)[source]
pySAXS.LS.LSsca.Pdqpoly(q1, FacePoly, sign, N)[source]
pySAXS.LS.LSsca.Pdqtetra(q, a, N)[source]
pySAXS.LS.LSsca.PolyGauss_ana_Norm(q, par)[source]

This fucntion calculates the normalized P(q) of a gaussian distribution of spheres centered in par[0] with an extension par[1] q array of q (A-1) par[0] Mean radius(A) par[1] Gaussian standard deviation (A)

pySAXS.LS.LSsca.PolySphere_int(q, Dfunc, par)[source]
pySAXS.LS.LSsca.Porod(q, B)[source]

Porod function q**-4*B*1e-32

pySAXS.LS.LSsca.Ppara(q, a, b, c)[source]

This function calculates the P(q) normalized to one at q=0 of a parallelepiped a,b,c (not finished 21/10/2009. this function makes use of dPpara which makes the integral over alpha

pySAXS.LS.LSsca.ProjSommets(Face)[source]
pySAXS.LS.LSsca.Qlogspace(qmin, qmax, np)[source]

This function returns an array of np q values evenlly separated in log scale between qmin and qmax

pySAXS.LS.LSsca.R(R, L, x, alp, b, x0)[source]
pySAXS.LS.LSsca.SHexa(R, L)[source]
pySAXS.LS.LSsca.SS(f, p)[source]

This function returns the specific surface of a distribution of spheres f function to compute the distribution p array of parameter

pySAXS.LS.LSsca.Scyl(R, L)[source]
pySAXS.LS.LSsca.SqSticky(q, R, eta, tao)[source]

This function computes the Baxter structure factor eta is the volume fraction tao is the sticky factor R is the radius in A q is an array of scattering vectors A-1

pySAXS.LS.LSsca.Surf(S)[source]
pySAXS.LS.LSsca.TFS(Sommets, a, b, qx, qy)[source]

returns the ff of polygon for a matrix qx,qy

pySAXS.LS.LSsca.TFSpi(Sommets, a, b, qx, qy)[source]

returns the ff of polygon for a matrix qx,qy

pySAXS.LS.LSsca.TFSs(Sommets, a, b, qx, qy)[source]

returns the ff of polygon for a scalar qx qy

pySAXS.LS.LSsca.Tetra1_Multiplet(b)[source]

b is the distance between spheres

pySAXS.LS.LSsca.Tetra2_Multiplet(c)[source]

c is the distance between the core and the satellites

pySAXS.LS.LSsca.Tetra_Multiplet(a)[source]

semble suspect

pySAXS.LS.LSsca.Tetraedre(a)[source]

returns the 3D coordinates of the 4 summits of a tetraedreof side length a

pySAXS.LS.LSsca.Triedre(a, L)[source]

return the 3D coordinates of the 6 submits of a triedre

pySAXS.LS.LSsca.Triplet_Multiplet(a)[source]
pySAXS.LS.LSsca.VHexa(R, L)[source]
pySAXS.LS.LSsca.Vcyl(R, L)[source]
pySAXS.LS.LSsca.Vcylcreuxcan(a, Ri, Ro, L)[source]
pySAXS.LS.LSsca.Vcylcreuxqcq(Ri, L, alp, b, x0, delt)[source]
pySAXS.LS.LSsca.amplitude_multiplet(q, L, rho, R)[source]
pySAXS.LS.LSsca.angle(teta, phi)[source]
pySAXS.LS.LSsca.dPcylb(qi, R, L, al)[source]
pySAXS.LS.LSsca.dPcylh(qi, R, L, al)[source]

Subfunction of Pcylh

pySAXS.LS.LSsca.dPpara(q, a, b, c, beta)[source]

Side function of Ppara

pySAXS.LS.LSsca.ddPcylh(qi, R, al)[source]

Sub-sub-function of dPcylh

pySAXS.LS.LSsca.distance(A, B)[source]
pySAXS.LS.LSsca.f(x, y)[source]
pySAXS.LS.LSsca.fP11_int(x, q, R, L)[source]
pySAXS.LS.LSsca.fP5_conc_int(x, q, R, e, rho)[source]
pySAXS.LS.LSsca.fP5_int(x, q, R, e)[source]
pySAXS.LS.LSsca.fPolySphere_int(R, q, Dfunc, Arg)[source]
pySAXS.LS.LSsca.fcan(x, y, z)[source]
pySAXS.LS.LSsca.fcanb(x, y, z)[source]
pySAXS.LS.LSsca.getRmoydist(R, D)[source]

This function returns the form factor of a dsitribution of spheres of radius R for q

pySAXS.LS.LSsca.getV(R)[source]

This function returns a the volume of a sphere with radius r

pySAXS.LS.LSsca.getVelli(R, e)[source]

This function returns a the volume of a sphere with radius r

pySAXS.LS.LSsca.pente(Sommets)[source]
pySAXS.LS.LSsca.qvectors(q, teta, phi)[source]
pySAXS.LS.LSsca.qvectorspi(q, teta, phi)[source]

LSusaxs Module

pySAXS routines for ultra small angle xray scattering. Lake deconvolution background substraction,...

version LSusaxs replacing LSreg by OT 7-2012 version 0.1 22/03/2006 version OS 20/11/2009

pySAXS.LS.LSusaxs.BackgroundCorrection(I, bkg)[source]
pySAXS.LS.LSusaxs.CalTransmission(mu_p, rho_p, mu_S, rho_S, phim_p, rho_soln, t)[source]

Calculates the transmission value for given sample parameters—

pySAXS.LS.LSusaxs.FitGauss(q, I, n, a0, a1, a2, tol=1e-15, it=2000)[source]
pySAXS.LS.LSusaxs.GoodnessOfFit(xexp, yexp, fmodel, par)[source]

This calculates the goodness of a fit

pySAXS.LS.LSusaxs.InterpolateForCommonvalue(qexp, Iexp, qrock, Irock)[source]
pySAXS.LS.LSusaxs.Qscalemod(dq, q, step)[source]
pySAXS.LS.LSusaxs.QtoTheta(q, wavelength)[source]
pySAXS.LS.LSusaxs.ThetatoQ(Theta, wavelength)[source]
pySAXS.LS.LSusaxs.TrCorrectedProf(qexp, Iexp, qrock, Irock, thickness, central_area, T)[source]

Transmission corrected profile

pySAXS.LS.LSusaxs.TransmissionValue(nsamp, nrock)[source]

calculate transmission : nsamp/nrock

pySAXS.LS.LSusaxs.USAXS_count_convolute(q, Iabs, N0dX, thick, wavelength)[source]

This subroutine calculates the counts that will be observed on USAXS for a particular model with q,I in cm-1

pySAXS.LS.LSusaxs.ZeroCentre(q, I)[source]
pySAXS.LS.LSusaxs.calculate_res_func_USAXS(filename, c, step, boun)[source]

This routine calculates the resolution function for the USAXS c is the slit length step is the step size for the V(beta) profile boun is the extreme left/right beta value for the V(beta) for which it shoule calculate the V(beta)

pySAXS.LS.LSusaxs.file_resfunc = 'C:\\Python27\\lib\\site-packages\\pySAXS\\saxsdata\\usaxs_res_func.dat'
def ReadUSAXSData(filename):
return SPio.array_import.read_array(filename,columns=(0,-2),lines=(1,-1))
def WriteUSAXSdata(filename,data):
return SPio.array_import.write_array(filename,data,separator=’ ‘)
pySAXS.LS.LSusaxs.gaussian(par, x)[source]
pySAXS.LS.LSusaxs.interpolate_res_func(x, resx=None, resy=None)[source]

Interpolated resolution function obtained from res_func.dat file if resx and resy are not None, use this datas

pySAXS.LS.LSusaxs.lake(qexp, Iexp, it, type, ns, m, resx, resy)[source]

Deconvolution subroutine based on Lake method

pySAXS.LS.LSusaxs.porod(par, q)[source]
pySAXS.LS.LSusaxs.read_res_function()[source]

read the resolution function from the specified filename

pySAXS.LS.LSusaxs.residuals(par, y, x)[source]
pySAXS.LS.LSusaxs.select(q, I, n)[source]

Selects the q,I for n points around the maximum

pySAXS.LS.LSusaxs.smooth(y, ns)[source]
pySAXS.LS.LSusaxs.somme(q, I)[source]

This gives the sum(I*delta q)

SAXSparametersOLD Module

project : pySAXS description : class for radial average parameters authors : Olivier Tache Last changes : Replaced by SAXSparameterXML 08-03-2007 OT : port to pySAXS library

class pySAXS.LS.SAXSparametersOLD.SAXSparametersOLD(printout=None)[source]
  • Radial Average Parameters -

wave_length=1.542 detector_to_sample=1 pixel_size=1 q_by_pixel=-1 exposition_time=1 backgd_by_s=0 #par seconde backgd_by_pix=0 #par pixel comment=”” transmission=-1 thickness=-1 K=1 monitor=1

calculBack()[source]

calculate background

calculDeltaOmega()[source]

calculate DeltaOmega

calculTotalFlux()[source]

calculate Flux

calculTransm()[source]

calculate Transmission

calculate_All()[source]

calculate all the function defined in paramsDesc

calculate_i(n, b=None, deviation=None, bdeviation=None)[source]

Calculate i in cm-1 from parameters n : raw intensity b : empty cell to substract deviation : absolute deviation for i bdeviation : absolute deviation for background ———————————– DeltaOmega=(pixel size / distance sample detector)^2 Flux = (monitor/transmission)*K Intensity=(n-background)/(time * DeltaOmega * Transmission * Thickness * Flux) if empty cell (b) then Final Intensity=( Intensity(with Thickness=1) - empty cell)/thickness

calculate_q(n)[source]

calculate q in A-1 from parameters n : pixel number ———————————- q=(4*pi/lambda)*sin(theta/2) with tan(theta)=d/D D : sample detector distance d : pixel number (n) * pixel size

calculate_q_by_pix()[source]

calculate q by pix in A-1 from parameters (RAP)

load(file_name)[source]
order()[source]

return a list with dictionnary key ordered

printTXT(txt='', par='')[source]
save(file_name)[source]
save_printable(file_name)[source]

SAXSparametersXML Module

project : pySAXS description : class for radial average parameters authors : Olivier Tache Last changes : 2012 : replacing the old SAXSparameters

IMPORTANT HERE : THE INITIALS PARAMETERS FOR ABSOLUTE SCALE

class pySAXS.LS.SAXSparametersXML.SAXSparameters(printout=None)[source]

Radial Average Parameters -

calculBack()[source]

calculate background

calculDeltaOmega()[source]

calculate DeltaOmega

calculTotalFlux()[source]

calculate Flux

calculTransm()[source]

calculate Transmission

calculate_All()[source]

calculate all the functions defined

calculate_i(n, b=None, deviation=None, bdeviation=None)[source]

Calculate i in cm-1 from parameters n : raw intensity b : empty cell to substract deviation : absolute deviation for i bdeviation : absolute deviation for background ———————————– DeltaOmega=(pixel size / distance sample detector)^2 Flux = (monitor/transmission)*K Intensity=(n-background)/(time * DeltaOmega * Transmission * Thickness * Flux) if empty cell (b) then Final Intensity=( Intensity(with Thickness=1) - empty cell)/thickness

calculate_q(n)[source]

calculate q in A-1 from parameters n : pixel number ———————————- q=(4*pi/lambda)*sin(theta/2) with tan(theta)=d/D D : sample detector distance d : pixel number (n) * pixel size

calculate_q_by_pix()[source]

calculate q by pix in A-1 from parameters (RAP)

eval_function(formula)[source]

return the evaluated value

get(variable)[source]

return the value of the specified variable

getFromXML(xmlElement)[source]

get parameters from xml element

goodCalculation()[source]

modify some parameter for good calculation : - backg=dbackgd_by_pix+backgd_by_s*time - transmission=TransmittedFlux/IncidentFlux - DeltaOmega=(pixel_size/D)**2 - flux=IncidentFlux*K

importOLD(filename)[source]

let us to import a old parameter file

load(file_name)[source]

load from a pickle (binary) file

openXML(filename)[source]

read from a xml file

order()[source]

return a list with dictionnary key ordered

printTXT(txt='', par='')[source]
save(file_name)[source]

save in a pickle (binary) file

saveXML(filename)[source]

save in a xml file

save_printable(file_name)[source]

save in a txt file

set(variable, value)[source]

change the value of the specified variable

xml()[source]

return an xml object

xmlString()[source]

return a xml string

class pySAXS.LS.SAXSparametersXML.parameter(name, value=None, description='', order=-1, formula=None, datatype=None, parent=None)[source]

class for parameters

eval()[source]

if self.evaluationFunction<>None: self.value=self.evaluationFunction() return self.value

get()[source]

return the value of the parameter

getfromXML(xmlElement)[source]

initialization given by xml element

set(value)[source]

set the value of the parameter

xml()[source]

return an element xml <time description=’time(s)’ order=‘2’ formula=’e=mc**2’ datatype=’float’>1.25</time>

absorption Module

pySAXS.LS.absorption.getAllMu()[source]

This function returns a big table with all NIST xray absorption data. For practical script it is not useful!

pySAXS.LS.absorption.getAtomsSymbole(S)[source]

Transform a string containing a chimical formula (‘C 1 O 2’) in two array - list of atoms - numeric array of atoms number 7-13-2012 by OT

pySAXS.LS.absorption.getAtomsSymboleOLD(S)[source]

Ceci est une fonction qui transforme une chaine de caracteres de formule chimique en deux tableaux l’un de chaine de caractere avec les symboles chimiques l’autre avec le nombre d’atome en question. version lourdo bugger pour le moment

pySAXS.LS.absorption.getElectronDensity(S, rho)[source]

return the electron density and the scattering length density

pySAXS.LS.absorption.getElectronNumber(S)[source]
pySAXS.LS.absorption.getMasseFormula(S, NRJ=8.028, ISEN=1)[source]

This function returns the molar mass a chemical formula in the form ‘C 6 H 6 O 2 N 1’ TODO improve getAtomsSymbole

pySAXS.LS.absorption.getMasseName(S)[source]

This function returns the molar mass of the atom with name S (ie ‘Carbon’ , ‘Gold’)

pySAXS.LS.absorption.getMasseSymbole(S)[source]

This function returns the molar mass of the atom with symble S (ie ‘C’ fo carbon, ‘Au’ for gold)

pySAXS.LS.absorption.getMasseZ(Z)[source]

This function returns the molar mass of the atom with atomic number Z

pySAXS.LS.absorption.getMuFormula(S, NRJ=8.028, ISEN=1)[source]

This function returns the mass attenuation coefficient for a chemical formula in the form ‘C 6 H 6 O 2 N 1’ 7-13-2012 by OT improved for formula with fraction ‘Si 1.2 Al 0.8’

pySAXS.LS.absorption.getMuName(S, NRJ=8.028, ISEN=1)[source]

This function returns the xray absorption coefficient of the atom with name S (ie ‘Carbon’ , ‘Gold’) by default NRJ is 8.028 keV and mass-energy absorption coefficient are return. To get the mass absorption coefficient ISEN has to be 0

pySAXS.LS.absorption.getMuSymbole(S, NRJ=8.028, ISEN=1)[source]

This function returns the xray absorption coefficient of the atom with symbole S (ie ‘C’ fo carbon, ‘Au’ for gold) by default NRJ is 8.03 keV and mass-energy absorption coefficient are return. To get the mass absorption coefficient ISEN has to be 0

pySAXS.LS.absorption.getMuZ(Z, NRJ=8.028, ISEN=1)[source]

This function returns the xray absorption coefficient of the atom with name S (ie ‘Carbon’ , ‘Gold’) by default NRJ is 8.028 keV and mass-energy absorption coefficient is returned. To get the mass absorption coefficient ISEN has to be 0

pySAXS.LS.absorption.setAtomsSymbole(atomS, atomN)[source]

Ceci est une fonction qui transforme une liste de symbole chimique et de nombre en une chaine de caractere.

absorptionXRL Module

This module use the xraylib library and provide high level functions for absorption factors for chemical compounds

August 2012 by OT based on work by AT

pySAXS.LS.absorptionXRL.getAngstFromSource(source='Cu')[source]

return the KA LINE (most used) energy in ANGSTROM from the x-ray source >>> getAngstFromSource(‘Cu’) 1.5418904085842968

pySAXS.LS.absorptionXRL.getAtomsFormula(S)[source]

Transform a string containing a chemical formula (‘C 1 O 2’) in two array - list of atoms - numeric array of atoms number 7-13-2012 by OT >>> getAtomsFormula(‘C 1 O 2’) [‘C’,’O’] [1,2]

pySAXS.LS.absorptionXRL.getElectronDensity(S, rho)[source]

return the electron density and the scattering length density

pySAXS.LS.absorptionXRL.getElectronNumber(S)[source]
pySAXS.LS.absorptionXRL.getEnergyFromSource(source='Cu')[source]

return the KA LINE (most used) energy from the x-ray source >>> getEnergyFromSource(‘Cu’) 8.04105057076251 >>> getEnergyFromSource(‘Mo’) 17.443217030477935

pySAXS.LS.absorptionXRL.getFormulaAtoms(atomS, atomN)[source]

transform a compound list and number in string >>> AtomsToCompound([‘H’,’O’],[2,1]) ‘H 2 O 1’

pySAXS.LS.absorptionXRL.getMasseFormula(S, energy=8.028)[source]

This function returns the molar mass a chemical formula in the form ‘C 6 H 6 O 2 N 1’

pySAXS.LS.absorptionXRL.getMasseSymbol(S)[source]

returns the molar mass (atomic weight) of the atom with atomic number Z (ie ‘C’ fo carbon, ‘Au’ for gold)

pySAXS.LS.absorptionXRL.getMasseZ(Z)[source]

returns the molar mass (atomic weight) of the atomic number Z

pySAXS.LS.absorptionXRL.getMuFormula(S, energy=8.028)[source]

This function returns the mass attenuation coefficient for a chemical formula in the form ‘C 6 H 6 O 2 N 1’

pySAXS.LS.absorptionXRL.getMuName(name, energy=8.028)[source]

This function returns the xray absorption coefficient of the atom with name S (ie ‘Carbon’ , ‘Gold’) by default energy is 8.028 keV and mass-energy absorption coefficient are return. To get the mass absorption coefficient

pySAXS.LS.absorptionXRL.getMuSymbol(S, energy=8.028)[source]

This function returns the xray absorption coefficient of the atom with symbole S (ie ‘C’ fo carbon, ‘Au’ for gold) by default energy is 8.03 keV and mass-energy absorption coefficient are return. To get the mass absorption coefficient ISEN has to be 0

pySAXS.LS.absorptionXRL.getMuZ(Z, energy=8.028)[source]

return Mu from Atomic number Z >>> getMuZ(4) 0.8719998598098755

pySAXS.LS.absorptionXRL.getNameZ(Z)[source]

return the name from a Z >>> getNameZ(29) ‘Copper’

pySAXS.LS.absorptionXRL.getTransmission(formula, thickness=1.0, density=1.0, energy=8.03)[source]

return the transmission of a compound thickness in cm >>> getTransmission(‘H 2 O 1’,0.1,density=1.0,energy=8.03) 0.376802369048

pySAXS.LS.absorptionXRL.getZName(name)[source]

return the Atomic Number Z from compound name >>> getZName(“Copper”) 29

invariant Module

calculation of invariant

class pySAXS.LS.invariant.invariant(q, i, printout=None, radius=300.0, verbose=True)[source]

class for calculation of invariant from data in i(q)

calculate(radius=None, qmin=None, qmax=None, extrapolation=None)[source]

calculate invariant and particle volume

calculateI0()[source]

calculate I0 I0 = Istar * exp(qmini ** 2 * radius ** 2 / 3.0) Istar is interpolation at qmin

getInvariant()[source]

return the calculate value use calculate() function before

getVolume()[source]

return the calculate volume for a particule use calculate() function before

printTXT(txt='', par='')[source]

for printing messages

rap Module

project : pySAXS description : class for radial average parameters authors : Olivier Tache Last changes : 08-03-2007 OT : port to pySAXS library

class pySAXS.LS.rap.RAP[source]
  • Radial Average Parameters -

beam_x : x beam position beam_y : y beam position roi_xmin, roi_ymin, roi_xmax, roi_ymax : #les points a masquer masks_list=[] : un tableau de roi geom_corr_x , geom_corr_y :correction geometrique wave_length=1.542 detector_to_sample=1 pixel_size=1 q_by_pixel=-1 exposition_time=1 backgd_by_s=0 #par seconde backgd_by_pix=0 #par pixel comment=”” transmission=-1 thickness=-1 K=1 monitor=1

Set_BeamXY(x, y)[source]
Set_ROI(xmin, ymin, xmax, ymax)[source]
calculate_q_by_pix()[source]

calculate q by pix in A-1 from parameters (RAP)

load(file_name)[source]
mask_add(polygon)[source]

ajoute un masque dans la liste des masques

mask_delete_all()[source]

efface la liste des masques

mask_remove(i)[source]

retire de la liste des masques l’element i

save(file_name)[source]
save_printable(file_name)[source]
pySAXS.LS.rap.Rad_Read(filename)[source]

Open the averaged data from a rgr file return qraw,q,iraw,i,n

pySAXS.LS.rap.Rad_Save(p, q, n, iq, filename)[source]

Save the averaged data in a rgr file wich can be opened by MS excel

pySAXS.LS.rap.calculate_q(q, par)[source]

calculate q in A-1 from parameters (RAP)